diff --git a/src/classes/PStartupHandler.cpp b/src/classes/PStartupHandler.cpp
index 5660ea88..6ce00364 100644
--- a/src/classes/PStartupHandler.cpp
+++ b/src/classes/PStartupHandler.cpp
@@ -178,10 +178,6 @@ void PStartupHandler::OnStartDocument()
   fFourierDefaults.fPlotRange[0] = -1.0;
   fFourierDefaults.fPlotRange[1] = -1.0;
   fFourierDefaults.fPhaseIncrement = 1.0;
-
-  fStartupOptions.writeExpectedChisq = false;
-  fStartupOptions.estimateN0 = true;
-  fStartupOptions.alphaEstimateN0 = 0.0;
 }
 
 //--------------------------------------------------------------------------
@@ -210,12 +206,6 @@ void PStartupHandler::OnStartElement(const Char_t *str, const TList *attributes)
 {
   if (!strcmp(str, "data_path")) {
     fKey = eDataPath;
-  } else if (!strcmp(str, "write_per_run_block_chisq")) {
-    fKey = eWritePerRunBlockChisq;
-  } else if (!strcmp(str, "estimate_n0")) {
-    fKey = eEstimateN0;
-  } else if (!strcmp(str, "alpha_estimate_n0")) {
-    fKey = eAlphaEstimateN0;
   } else if (!strcmp(str, "marker")) {
     fKey = eMarker;
   } else if (!strcmp(str, "color")) {
@@ -270,21 +260,6 @@ void PStartupHandler::OnCharacters(const Char_t *str)
       // add str to the path list
       fDataPathList.push_back(str);
       break;
-    case eWritePerRunBlockChisq:
-      tstr = TString(str);
-      if (tstr.BeginsWith("y") || tstr.BeginsWith("Y"))
-        fStartupOptions.writeExpectedChisq = true;
-      break;
-    case eEstimateN0:
-      tstr = TString(str);
-      if (tstr.BeginsWith("n") || tstr.BeginsWith("N"))
-        fStartupOptions.estimateN0 = false;
-      break;
-    case eAlphaEstimateN0:
-      tstr = TString(str);
-      if (tstr.IsFloat())
-        fStartupOptions.alphaEstimateN0 = tstr.Atof();
-      break;
     case eMarker:
       // check that str is a number
       tstr = TString(str);
diff --git a/src/include/PMusr.h b/src/include/PMusr.h
index 96df487f..d093cbfa 100644
--- a/src/include/PMusr.h
+++ b/src/include/PMusr.h
@@ -815,12 +815,11 @@ typedef struct {
 
 //-------------------------------------------------------------
 /**
- * <p>Holds the informations for the any2many converter program
+ * <p>Holds the informations
  */
 typedef struct {
   Bool_t writeExpectedChisq; ///< if set to true, expected chisq per block will be written
   Bool_t estimateN0;         ///< if set to true, for single histogram fits N0 will be estimated
-  Double_t alphaEstimateN0;  ///< relates the Bkg to N0, i.e. Bkg = alpha*N0
 } PStartupOptions;
 
 //-------------------------------------------------------------
diff --git a/src/include/PStartupHandler.h b/src/include/PStartupHandler.h
index 9125a67b..89602014 100644
--- a/src/include/PStartupHandler.h
+++ b/src/include/PStartupHandler.h
@@ -73,17 +73,15 @@ class PStartupHandler : public TObject, public TQObject
 
     virtual void CheckLists();
 
-    virtual PStartupOptions* GetStartupOptions() { return &fStartupOptions; } ///< returns the startup options
     virtual PMsrFourierStructure  GetFourierDefaults() { return fFourierDefaults; } ///< returns the Fourier defaults
     virtual const PStringVector   GetDataPathList() const { return fDataPathList; } ///< returns the search data path list
     virtual const PIntVector      GetMarkerList() const { return fMarkerList; }     ///< returns the marker list
     virtual const PIntVector      GetColorList() const { return fColorList; }       ///< returns the color list
 
-    virtual void SetStartupOptions(const PStartupOptions opt) { fStartupOptions = opt; }
-
   private:
-    enum EKeyWords {eEmpty, eComment, eDataPath, eOptions, eWritePerRunBlockChisq, eEstimateN0, eAlphaEstimateN0,
-                    eFourierSettings, eUnits, eFourierPower, eApodization, ePlot, ePhase, ePhaseIncrement,
+    enum EKeyWords {eEmpty, eComment, eDataPath, eOptions,
+                    eFourierSettings, eUnits, eFourierPower,
+                    eApodization, ePlot, ePhase, ePhaseIncrement,
                     eRootSettings, eMarkerList, eMarker, 
                     eColorList, eColor};
     EKeyWords       fKey; ///< xml filter key
@@ -94,7 +92,6 @@ class PStartupHandler : public TObject, public TQObject
     PStringVector        fDataPathList;     ///< search data path list
     PIntVector           fMarkerList;       ///< marker list
     PIntVector           fColorList;        ///< color list
-    PStartupOptions      fStartupOptions;   ///< collects all startup options which will be requested by PMsrFileHandler
 
     Bool_t StartupFileExists(Char_t *fln);
 
diff --git a/src/musrfit.cpp b/src/musrfit.cpp
index 0bb0bd2d..aa6200a1 100644
--- a/src/musrfit.cpp
+++ b/src/musrfit.cpp
@@ -104,9 +104,8 @@ void musrfit_syntax()
   cout << endl << "       -t, --title-from-data-file: will replace the <msr-file> run title by the";
   cout << endl << "              run title of the FIRST run of the <msr-file> run block, if a run title";
   cout << endl << "              is present in the data file.";
-  cout << endl << "       -e, --estimateN0: estimate N0 for single histogram fits flag. <flag> can have the values 'yes' or 'no'.";
+  cout << endl << "       -e, --estimateN0: estimate N0 for single histogram fits.";
   cout << endl << "       -p, --per-run-block-chisq: will write per run block chisq to the msr-file.";
-  cout << endl << "              <flag> can have the values 'yes' or 'no'.";
   cout << endl << "       --dump <type> is writing a data file with the fit data and the theory";
   cout << endl << "              <type> can be 'ascii', 'root'";
   cout << endl << "       --timeout <timeout_tag>: overwrites to predefined timeout of " << timeout << " (sec).";
@@ -444,8 +443,7 @@ int main(int argc, char *argv[])
   bool timeout_enabled = true;
   PStartupOptions startup_options;
   startup_options.writeExpectedChisq = false;
-  startup_options.estimateN0 = true;
-  startup_options.alphaEstimateN0 = 0.0;
+  startup_options.estimateN0 = false;
 
   TString dump("");
   char filename[1024];
@@ -496,39 +494,9 @@ int main(int argc, char *argv[])
         break;
       }
     } else if (!strcmp(argv[i], "-e") || !strcmp(argv[i], "--estimateN0")) {
-      if (i<argc-1) {
-        if (!strcmp(argv[i+1], "yes")) {
-          startup_options.estimateN0 = true;
-        } else if (!strcmp(argv[i+1], "no")) {
-          startup_options.estimateN0 = false;
-        } else {
-          cerr << endl << "musrfit: **ERROR** option --estimateN0 <flag> with unsupported <flag> = " << argv[i+1] << endl;
-          show_syntax = true;
-          break;
-        }
-        i++;
-      } else {
-        cerr << endl << "musrfit: **ERROR** found option --estimateN0 without <flag>" << endl;
-        show_syntax = true;
-        break;
-      }
+      startup_options.estimateN0 = true;
     } else if (!strcmp(argv[i], "-p") || !strcmp(argv[i], "--per-run-block-chisq")) {
-      if (i<argc-1) {
-        if (!strcmp(argv[i+1], "yes")) {
-          startup_options.writeExpectedChisq = true;
-        } else if (!strcmp(argv[i+1], "no")) {
-          startup_options.writeExpectedChisq = false;
-        } else {
-          cerr << endl << "musrfit: **ERROR** option --per-run-block-chisq <flag> with unsupported <flag> = " << argv[i+1] << endl;
-          show_syntax = true;
-          break;
-        }
-        i++;
-      } else {
-        cerr << endl << "musrfit: **ERROR** found option --per-run-block-chisq without <flag>" << endl;
-        show_syntax = true;
-        break;
-      }
+      startup_options.writeExpectedChisq = true;
     } else if (!strcmp(argv[i], "--timeout")) {
       if (i<argc-1) {
         TString str(argv[i+1]);
@@ -614,13 +582,11 @@ int main(int argc, char *argv[])
       }
     }
   }
-  if (startupHandler)
-    startupHandler->SetStartupOptions(startup_options);
 
   // read msr-file
   PMsrHandler *msrHandler = 0;
   if (startupHandler)
-    msrHandler = new PMsrHandler(filename, startupHandler->GetStartupOptions());
+    msrHandler = new PMsrHandler(filename, &startup_options);
   else
     msrHandler = new PMsrHandler(filename);
   status = msrHandler->ReadMsrFile();
diff --git a/src/musrfit_startup.xml b/src/musrfit_startup.xml
index daf13703..3aa5ab57 100644
--- a/src/musrfit_startup.xml
+++ b/src/musrfit_startup.xml
@@ -14,11 +14,6 @@
     <data_path>/afs/psi.ch/project/bulkmusr/data/alc</data_path>
     <data_path>/afs/psi.ch/project/bulkmusr/data/hifi</data_path>
     <data_path>/afs/psi.ch/project/bulkmusr/data/lem</data_path>
-    <options>
-      <write_per_run_block_chisq>n</write_per_run_block_chisq>
-      <estimate_n0>yes</estimate_n0>
-      <alpha_estimate_n0>0.0</alpha_estimate_n0>      
-    </options>
     <fourier_settings>
         <units>Gauss</units>
         <fourier_power>0</fourier_power>